[ensembl-dev] Problem with gtf2vep.pl

Will McLaren wm2 at ebi.ac.uk
Wed Jan 8 13:23:41 GMT 2014


Hello Alan,

Thanks for the detailed report. There's an odd bug happening here which I
can't get to the bottom of at the moment.

I've added a fix for now which stops the error happening, and the cache
builds fine for me from your input.

Since we're in the process of switching our code hosting to Git, for now I
have only pushed the fix to our GitHub - you can get the fixed script here:

https://github.com/Ensembl/ensembl-tools/blob/release/74/scripts/variant_effect_predictor/gtf2vep.pl

Let me know if this isn't convenient and I can get the fix pushed to our
CVS tree too.

PS I assume you are aware we build a cache file for macaque already?
ftp://ftp.ensembl.org/pub/release-74/variation/VEP/

Thanks again

Will McLaren
Ensembl Variation


On 8 January 2014 05:38, Harris, Ronald Alan <rharris1 at bcm.edu> wrote:

>   Hi,
>
> I have been trying to use gtf2vep.pl to generate a cache file based
> on RhesusBase (http://www.rhesusbase.org/) gene annotations on the UCSCrheMac2
> /Ensembl MMUL_1 assembly. I downloaded their rb2 gene predictions as a gtffile through their UCSCmirror, changed the source column to "protein_coding",
> added "exon_number" and the appropriate number in the description field,
> and sorted the annotations by chromosome position. The gtf file can be
> downloaded from here:
>
>
> https://bigfile.bcm.edu/download.php?claimID=tnwUAesf9rRRH3u5&claimPasscode=B8mm8RNVZG4Ub6Xy&fid=52811&emailAddr=rharris1@bcm.edu
>
> When I run gtf2vep.pl I get this error:
>
> Can't call method "start" on an undefined value at gtf2vep.pl line 376.
>
> This error occurs after generating some of the cache files in the .vepdirectory. I tried to run
> gtf2vep.pl using gtf files with only a single chromosome and it looks
> like the error consistently occurs when trying to generate the 1-1000000
> cache file. Oddly, if I just run gtf2vep.pl on the annotations from
> 1-1000000 on a single chromosome I do not get this error.
>
> I don't think this is due to chr in chromosome names because the fastafile I am using has chrin the chromosome names.
>
> I would appreciate any help you could give me with this.
>
> Thanks,
>
> Alan
>
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